Ejemplo n.º 1
0
def sample(batch_id):
    NCV_db = NCV.query.filter(NCV.batch_id == batch_id)
    sample_db = Sample.query.filter(Sample.batch_id == batch_id)
    batch = Batch.query.filter(Batch.batch_id == batch_id).first()
    DC = DataClasifyer()
    DC.handle_NCV(NCV_db)
    DC.get_QC_warnings(sample_db)
    DC.get_manually_classified(sample_db)
    PP = PlottPage(batch_id)
    PP.make_NCV_stat()
    PP.make_chrom_abn()
    PP.make_cov_plot_data()
    return render_template('batch_page.html',
        NCV_samples     = NCV.query.filter(NCV.batch_id == batch_id),
        batch_name      = batch.batch_name,
        man_class       = DC.man_class,
        NCV_stat        = PP.NCV_stat,
        NCV_sex         = DC.NCV_sex,
        seq_date        = batch.date,
        nr_validation_samps = PP.nr_validation_samps,
        samp_range      = range(len(PP.NCV_stat['NCV_X']['NCV_cases'])),
        tris_chrom_abn  = PP.tris_chrom_abn,
        sex_chrom_abn   = PP.sex_chrom_abn,
        abn_status_list = ['Verified','False Positive', 'Probable', 'Suspected'],
        many_colors     = PP.many_colors,
        sex_abn_colors  = PP.sex_abn_colors,
        sex_tresholds   = DC.sex_tresholds,
        tris_thresholds = DC.tris_thresholds,
        seq_warnings = DC.QC_warnings,
        warnings = DC.NCV_classified,
        NCV_rounded = DC.NCV_data,
        samp_cov_db = PP.coverage_plot,
        sample_ids = ','.join(sample.sample_ID for sample in NCV_db))
Ejemplo n.º 2
0
def sample_page( sample_id):
    sample = Sample.query.filter_by(sample_ID = sample_id).first()
    batch_id = sample.batch_id
    batch = Batch.query.filter_by(batch_id = batch_id).first()
    NCV_db = NCV.query.filter(NCV.batch_id == batch_id)
    DC = DataClasifyer()
    DC.handle_NCV(NCV_db)
    NCV_dat = NCV.query.filter_by(sample_ID = sample_id).first()
    chrom_abnorm = ['T13','T18', 'T21', 'X0', 'XXX','XXY','XYY']
    db_entries = {c:sample.__dict__['status_'+c].replace('\r\n', '').strip() for c in chrom_abnorm }
    db_entries_change = {c:sample.__dict__['status_change_'+c]  for c in chrom_abnorm}              
    db_entries_comments = {c : sample.__dict__['comment_'+c]  for c in chrom_abnorm}
    PP = PlottPage(batch_id)
    PP.make_NCV_stat()
    PP.make_chrom_abn()
    sample_state_dict = PP.sample_state_dict
    for state in sample_state_dict:
        sample_state_dict[state]['T_13'] = Sample.query.filter_by(status_T13 = state)
        sample_state_dict[state]['T_18'] = Sample.query.filter_by(status_T18 = state)
        sample_state_dict[state]['T_21'] = Sample.query.filter_by(status_T21 = state)
    return render_template('sample_page.html',
            NCV_dat = NCV_dat,
            tris_abn = PP.tris_abn,
            sex_chrom_abn = PP.sex_chrom_abn,
            abn_status_list = ['Verified','False Positive', 'Probable', 'Suspected'],
            sex_abn_colors  = PP.sex_abn_colors,
            sample = sample, 
            NCV_db = NCV.query.filter_by(sample_ID = sample_id).first(), 
            batch_id = batch_id,
            batch_name = batch.batch_name,
            batch = batch,
            nr_validation_samps = PP.nr_validation_samps,
            sample_id = sample_id,
            chrom_abnorm = chrom_abnorm,
            db_entries = db_entries,
            db_entries_comments = db_entries_comments,
            db_entries_change = db_entries_change,
            NCV_stat = PP.NCV_stat,
            NCV_131821 = ['NCV_13', 'NCV_18', 'NCV_21'],
            state_dict = sample_state_dict,
            sex_tresholds = DC.sex_tresholds,
            tris_thresholds = DC.tris_thresholds,
            NCV_sex = DC.NCV_sex[sample_id],
            NCV_warn = DC.NCV_classified[sample_id])
Ejemplo n.º 3
0
def sample_page( sample_id):
    sample = Sample.query.filter_by(sample_ID = sample_id).first()
    batch_id = sample.batch_id
    batch = Batch.query.filter_by(batch_id = batch_id).first()
    NCV_db = NCV.query.filter(NCV.batch_id == batch_id)
    DC = DataClasifyer(NCV_db)
    DC.handle_NCV()
    DC.make_sex_tresholds(BDF.NCV_passed_X) 
    NCV_dat = NCV.query.filter_by(sample_ID = sample_id).first()
    chrom_abnorm = ['T13','T18', 'T21', 'X0', 'XXX','XXY','XYY']
    db_entries = {c:sample.__dict__['status_'+c].replace('\r\n', '').strip() for c in chrom_abnorm }
    db_entries_change = {c:sample.__dict__['status_change_'+c]  for c in chrom_abnorm}              
    PP = PlottPage(batch_id, BDF)
    PP.make_NCV_stat()
    PP.make_chrom_abn()
    return render_template('sample_page.html',
        ## Header & Info Box
        NCV_dat         = NCV_dat,
        sample          = sample,
        batch_id        = batch_id,
        batch_name      = batch.batch_name,
        batch           = batch,
        NCV_sex         = DC.NCV_sex[sample_id],
        NCV_warn        = DC.NCV_classified[sample_id],
        ## Comment
        NCV_db          = NCV.query.filter_by(sample_ID = sample_id).first(),
        ## NCV Table
        sample_id       = sample_id,
        chrom_abnorm    = chrom_abnorm,
        db_entries      = db_entries,
        db_entries_change = db_entries_change,
        ## Plots
        tris_abn        = PP.tris_abn,
        sex_chrom_abn   = PP.sex_chrom_abn,
        case_size       = PP.case_size,
        abn_size        = PP.abn_size,
        abn_status_list = ['Other','False Positive','Suspected', 'Probable', 'Verified'],
        ncv_abn_colors  = PP.ncv_abn_colors,
        NCV_stat        = PP.NCV_stat,
        NCV_131821      = ['NCV_13', 'NCV_18', 'NCV_21'],
        sex_tresholds   = DC.sex_tresholds,
        tris_thresholds = DC.tris_thresholds,
        tris_chrom_abn  = PP.tris_chrom_abn)
Ejemplo n.º 4
0
def sample_page(sample_id):
    sample = Sample.query.filter_by(sample_ID=sample_id).first()
    batch_id = sample.batch_id
    batch = Batch.query.filter_by(batch_id=batch_id).first()
    NCV_db = NCV.query.filter(NCV.batch_id == batch_id)
    DC = DataClasifyer()
    DC.handle_NCV(NCV_db)
    NCV_dat = NCV.query.filter_by(sample_ID=sample_id).first()
    chrom_abnorm = ['T13', 'T18', 'T21', 'X0', 'XXX', 'XXY', 'XYY']
    db_entries = {
        c: sample.__dict__['status_' + c].replace('\r\n', '').strip()
        for c in chrom_abnorm
    }
    db_entries_change = {
        c: sample.__dict__['status_change_' + c]
        for c in chrom_abnorm
    }
    db_entries_comments = {
        c: sample.__dict__['comment_' + c]
        for c in chrom_abnorm
    }
    PP = PlottPage(batch_id)
    PP.make_NCV_stat()
    PP.make_chrom_abn()
    sample_state_dict = PP.sample_state_dict
    for state in sample_state_dict:
        sample_state_dict[state]['T_13'] = Sample.query.filter_by(
            status_T13=state)
        sample_state_dict[state]['T_18'] = Sample.query.filter_by(
            status_T18=state)
        sample_state_dict[state]['T_21'] = Sample.query.filter_by(
            status_T21=state)
    return render_template(
        'sample_page.html',
        NCV_dat=NCV_dat,
        tris_abn=PP.tris_abn,
        sex_chrom_abn=PP.sex_chrom_abn,
        abn_status_list=[
            'Verified', 'False Positive', 'Probable', 'Suspected'
        ],
        sex_abn_colors=PP.sex_abn_colors,
        sample=sample,
        NCV_db=NCV.query.filter_by(sample_ID=sample_id).first(),
        batch_id=batch_id,
        batch_name=batch.batch_name,
        batch=batch,
        nr_validation_samps=PP.nr_validation_samps,
        sample_id=sample_id,
        chrom_abnorm=chrom_abnorm,
        db_entries=db_entries,
        db_entries_comments=db_entries_comments,
        db_entries_change=db_entries_change,
        NCV_stat=PP.NCV_stat,
        NCV_131821=['NCV_13', 'NCV_18', 'NCV_21'],
        state_dict=sample_state_dict,
        sex_tresholds=DC.sex_tresholds,
        tris_thresholds=DC.tris_thresholds,
        NCV_sex=DC.NCV_sex[sample_id],
        NCV_warn=DC.NCV_classified[sample_id])
Ejemplo n.º 5
0
def sample(batch_id):
    NCV_db = NCV.query.filter(NCV.batch_id == batch_id)
    sample_db = Sample.query.filter(Sample.batch_id == batch_id)
    batch = Batch.query.filter(Batch.batch_id == batch_id).first()
    DC = DataClasifyer(NCV_db)
    DC.handle_NCV()
    DC.make_sex_tresholds(BDF.NCV_passed_X)
    DC.get_QC_warnings(sample_db)
    DC.get_manually_classified(sample_db)
    PP = PlottPage(batch_id, BDF)
    PP.make_NCV_stat()
    PP.make_chrom_abn()
    PP.make_cov_plot_data()
    return render_template('batch_page.html',
        ##  Header
        batch_name      = batch.batch_name,        
        seq_date        = batch.date,
        ##  Warnings Table
        seq_warnings    = DC.QC_warnings,
        ##  NCV Table
        NCV_samples     = NCV.query.filter(NCV.batch_id == batch_id),
        man_class       = DC.man_class_merged,
        NCV_sex         = DC.NCV_sex,
        warnings        = DC.NCV_classified,
        NCV_rounded     = DC.NCV_data,
        ##  Plotts
        NCV_stat        = PP.NCV_stat,
        case_size       = PP.case_size,
        abn_size        = PP.abn_size,
        samp_range      = range(len(PP.NCV_stat['NCV_X']['NCV_cases'])),
        tris_chrom_abn  = PP.tris_chrom_abn,
        sex_chrom_abn   = PP.sex_chrom_abn,
        abn_status_list = ['Other','False Positive','Suspected', 'Probable', 'Verified'],
        cov_colors      = PP.cov_colors,
        many_colors     = PP.many_colors,
        ncv_abn_colors  = PP.ncv_abn_colors,
        sex_tresholds   = DC.sex_tresholds,
        tris_thresholds = DC.tris_thresholds,
        ##  Coverage
        bool_warns      = filter(None, DC.NCV_classified.values()),
        samp_cov_db     = PP.coverage_plot,
        ##  Buttons
        batch_id        = batch_id,
        sample_ids      = ','.join(sample.sample_ID for sample in NCV_db))
Ejemplo n.º 6
0
def sample(batch_id):
    NCV_db = NCV.query.filter(NCV.batch_id == batch_id)
    sample_db = Sample.query.filter(Sample.batch_id == batch_id)
    batch = Batch.query.filter(Batch.batch_id == batch_id).first()
    DC = DataClasifyer()
    DC.handle_NCV(NCV_db)
    DC.get_QC_warnings(sample_db)
    DC.get_manually_classified(sample_db)
    PP = PlottPage(batch_id)
    PP.make_NCV_stat()
    PP.make_chrom_abn()
    PP.make_cov_plot_data()
    return render_template(
        'batch_page.html',
        NCV_samples=NCV.query.filter(NCV.batch_id == batch_id),
        batch_name=batch.batch_name,
        man_class=DC.man_class,
        NCV_stat=PP.NCV_stat,
        NCV_sex=DC.NCV_sex,
        seq_date=batch.date,
        nr_validation_samps=PP.nr_validation_samps,
        samp_range=range(len(PP.NCV_stat['NCV_X']['NCV_cases'])),
        tris_chrom_abn=PP.tris_chrom_abn,
        sex_chrom_abn=PP.sex_chrom_abn,
        abn_status_list=[
            'Verified', 'False Positive', 'Probable', 'Suspected'
        ],
        many_colors=PP.many_colors,
        sex_abn_colors=PP.sex_abn_colors,
        sex_tresholds=DC.sex_tresholds,
        tris_thresholds=DC.tris_thresholds,
        seq_warnings=DC.QC_warnings,
        warnings=DC.NCV_classified,
        NCV_rounded=DC.NCV_data,
        samp_cov_db=PP.coverage_plot,
        sample_ids=','.join(sample.sample_ID for sample in NCV_db))